diff --git a/pybedlite/overlap_detector.py b/pybedlite/overlap_detector.py index fd77c54..7b85b8a 100644 --- a/pybedlite/overlap_detector.py +++ b/pybedlite/overlap_detector.py @@ -2,25 +2,24 @@ Utility Classes for Querying Overlaps with Genomic Regions ---------------------------------------------------------- - The :class:`~pybedlite.overlap_detector.OverlapDetector` class detects and returns overlaps between -a set of regions and another region on a reference. The overlap detector may contain any -interval-like Python objects that have the following properties: +a set of regions and another region on a reference. The overlap detector may contain a collection +of interval-like Python objects that have the following properties: * `refname` (str): The reference sequence name * `start` (int): A 0-based start position * `end` (int): A 0-based exclusive end position -This is encapsulated in the :class:`~pybedlite.overlap_detector.Span` protocol. +This contract is described by the :class:`~pybedlite.overlap_detector.Span` protocol. Interval-like Python objects may also contain strandedness information which will be used for sorting them in :func:`~pybedlite.overlap_detector.OverlapDetector.get_overlaps` using -the following property if it is present, otherwise assumed to be positive stranded: +the following property if it is present: * `negative (bool)`: True if the interval is negatively stranded, False if the interval is unstranded or positively stranded -This is encapsulated in the :class:`~pybedlite.overlap_detector.StrandedSpan` protocol. +This contract is described by the :class:`~pybedlite.overlap_detector.StrandedSpan` protocol. Examples of Detecting Overlaps ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~